Installating VASP on 64-bit AMD Opteron Cluster CentOS 5 Linux

From their website.

VAMP/VASP [Vienna Ab-initio Simulation Package] is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing. These techniques avoid all problems occurring in the original Car-Parrinello method which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described using ultrasoft Vanderbilt pseudopotentials (US-PP) or the projector augmented wave method (PAW). Both techniques allow a considerable reduction of the necessary number of plane-waves per atom for transition metals and first row elements. Forces and stress can be easily calculated with VAMP/VASP and used to relax atoms into their instantaneous groundstate.

Or, in other words...

Bahasa Indonesian Lesson Four

Body Language and Conversation

Conservative dressing in Indonesia consists of a collared shirt for men and long pants. Women are expected also to wear pants or skirts that go beyond the knee and tops which cover the shoulder. Shorts and t-shirts are accepted in tourist areas and bikinis on tourits beaches, but otherwise they are best avoided, and certainly must be avoided when visiting an Indonesian home or place of worship. Sarongs, short-pants and t-shirts are normally worn around the home. In Balinese Hindu temples, a sash should be worn around the waist.

Bahasa Indonesian Lesson Three


Prepositions establish relationships between words and are therefore useful in building phrases. Some common examples in Bahasa Indonesia include the following:

At, In, On (all referring to place), use "Di".
At, In, On, For (all referring to time, use "Pada jam", "Dalam", "Pada", "Selama", respectively.
For (a purpose) use "Untuk"
From use "Dari"
Towards use "Ke"
Inside, Outside use "Di dalam", "Di luar", respectively
Since and Until use "Sejak", "Sampai", respectively
About and With use "Tentang" and "Dengan", respectively

Bahasa Indonesian Lesson Two

Greetings and Responses

In any language basic introductions must be learned. Introductions in Indonesia may include a gentle handshake and the touching of the heart afterwards to indicate goodwill. Always use the right hand.

"Selamat" is the basic greeting word, derived from the Arabic "salam", meaning peace.

"Selamat pagi" (Good morning), "Selamat siang" (Good day, from about 11am to 2-3pm), "Selamat sore" (Good afternoon), "Selamat malam (good evening, after nightfall), "Selamat tidur" (good night, "tidur" = to sleep).

Bahasa Indonesian Lesson One

Whilst rote-learning should be avoided in most cases when learning a second language in some cases, as people learn sentences, not words, in some basic cases it is an effective way to ingrain knowledge. Specifically, basic pronunciation, the alphabet and numbers should be practised until they become second nature.


Mesa and LIBDRM on a 64 bit Opteron Fedora Core 5 Cluster

Further adventures in attempting to install Underworld 1.2 on Wexstan.

Previous instruction for installing Mesa largely work, but with the following exceptions.

Use a new directory name and run the configuration as modified...

mkdir -p /usr/local/mesa/7.4
./configure --prefix=/usr/local/mesa/7.4-gcc

... and discover a new and interesting failure.

checking for LIBDRM... configure: error: Package requirements (libdrm >= 2.4.3) were not met:

PETSc on a 64 bit Opteron Fedora Core 5 Cluster

Wextan is a 64 bit Opteron Linux Cluster with 32 Opteron 246 CPUS with 64 Gb Ram and 0.5 Terabytes of Hard Disk Storage running Fedora Core 5. A user wants to install Underworld v1.2 on this machine.

Installing 32 and 64 -bit Versions of Mesa Graphics Library

Mesa (why does their website use frames?) is an open source 3D graphics library based on the OGL specification. It's been around since 1993 and is still in regular development, making it quite popular for scientific applications.

Installing NAMD 2.7b1 on a 64-bit AMD Opteron Cluster running CentOS 5 Linux

NAMD is a parallel molecular dynamics code for large biomolecular systems. Version 2.7b1 has some advantages over 2.6 and an extensive user's guide.

Download the tarball (registration required), put it somewhere sensible (e.g., /usr/local/src/NAMD) and unpack (tar xvf NAMD_2.7b1_Source.tar.gz) and enter that directory.


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